## 
## Attaching package: 'lubridate'
## The following objects are masked from 'package:base':
## 
##     date, intersect, setdiff, union

1 Analysis

## 
## Attaching package: 'plotly'
## The following object is masked from 'package:ggplot2':
## 
##     last_plot
## The following object is masked from 'package:stats':
## 
##     filter
## The following object is masked from 'package:graphics':
## 
##     layout
## Warning: Specifying width/height in layout() is now deprecated.
## Please specify in ggplotly() or plot_ly()

2 Correlation

Correlation of growth and duration: -0.2853115

# install.packages("caret")
library(caret)
## Loading required package: lattice
preproc = preProcess(converged)
norm = predict(preproc, converged)
dist = dist(norm, method="euclidian")
## Warning in dist(norm, method = "euclidian"): NAs introduced by coercion
hc = hclust(dist, method="ward.D")
# plot(hc)
clusters = cutree(hc, k=4)
table(clusters)
## clusters
##  1  2  3  4 
## 39 15 14  1
c1 = subset(converged, clusters==1)
c1$country 
##  [1] Andorra             Antigua and Barbuda Austria            
##  [4] Barbados            Botswana            Bulgaria           
##  [7] Croatia             Cuba                Cyprus             
## [10] Czechia             Denmark             Diamond Princess   
## [13] Djibouti            Eritrea             Estonia            
## [16] Eswatini            Greece              Hungary            
## [19] Iceland             Ireland             Israel             
## [22] Kosovo              Laos                Latvia             
## [25] Lebanon             Lithuania           Luxembourg         
## [28] Montenegro          Netherlands         New Zealand        
## [31] Niger               Norway              Poland             
## [34] Portugal            San Marino          Serbia             
## [37] Switzerland         Tunisia             Uruguay            
## 187 Levels: Afghanistan Albania Algeria Andorra Angola ... Zimbabwe
# c1: Small countries successfull fighting quickly
c2 = subset(converged, clusters==2)
c2$country 
##  [1] Angola                           Brunei                          
##  [3] Chile                            Ecuador                         
##  [5] Fiji                             Holy See                        
##  [7] Liechtenstein                    Nepal                           
##  [9] Papua New Guinea                 Saint Kitts and Nevis           
## [11] Saint Vincent and the Grenadines Slovenia                        
## [13] Suriname                         Timor-Leste                     
## [15] Venezuela                       
## 187 Levels: Afghanistan Albania Algeria Andorra Angola ... Zimbabwe
# c2: Very small countries successfull fighting quickly
c3 = subset(converged, clusters==3)
c3$country 
##  [1] Australia    Belgium      Canada       Finland      Germany     
##  [6] Iran         Italy        Korea, South Russia       Spain       
## [11] Sri Lanka    Taiwan*      Thailand     Turkey      
## 187 Levels: Afghanistan Albania Algeria Andorra Angola ... Zimbabwe
# c3: Misc.
c4 = subset(converged, clusters==4)
c4$country 
## [1] US
## 187 Levels: Afghanistan Albania Algeria Andorra Angola ... Zimbabwe
# c4: Large countries

From https://www.cidrap.umn.edu/sites/default/files/public/downloads/cidrap-covid19-viewpoint-part1.pdf average incubation period for COVID-19 is 5 days (range, 2 to 14 days) (Lauer 2020). The longer incubation period for COVID-19 allowed the virus to move silently in different populations before being detected (Kahn 2020, Li 2020). This contributed to an initial environment of complacency before national governments became aware of the severity of the situation The second important factor is the asymptomatic fraction for the two infections. Although information is still being collected to definitively define the asymptomatic fraction for COVID-19, public health officials have stated that 25% of all cases may be asymptomatic (Rettner 2020) and better serologic studies may revise this percentage upward. A number of studies have explored the asymptomatic fraction for influenza; one review found a pooled mean for the asymptomatic fraction of 16% (range of 4% to 28%) (Leung 2015). Thus, while both viruses can lead to asymptomatic infections, the asymptomatic fraction appears to be somewhat higher for COVID-19 than for influenza

Another consideration is the timeframe of presymptomatic viral shedding for people who fall ill. One recent study found that the SARS-CoV-2 viral load was highest at the time of symptom onset, suggesting that viral shedding may peak before symptoms occur, leading to substantial presymptomatic transmission (He 2020). A point-prevalence study of SARS-CoV-2 in nursing home residents showed that, for 27 residents who were asymptomatic at the time of testing, 24 developed symptoms a median of 4 days later (interquartile range, 3 to 5 days) (Arons 2020), supporting the potential for several days of presymptomatic shedding. For the H1N1 pandemic influenza